Fig. 6: Cdx2 modifies chromatin access in regions with critical differentiation factors.

a Number of ATAC-Seq peaks found in Scl-Cre and Scl:Cdx2 BM LKS+ cells. b Centrally enriched motifs in peaks specific for Scl:Cdx2 BM samples by ATAC-Seq and Cdx2-FLAG BM samples by ChIP-Seq (as labeled) determined by MEME Suite. c Heatmaps of the top 1000 gained peaks at distal elements (peak centres +/− 2000 base pairs) that overlap between Cdx2-Flag BM samples by ChIP-Seq and Scl:Cdx2 or Scl-Cre BM samples by ATAC-Seq, ordered by signal intensity. LKS, CMP, GMP ATAC-Seq read coverage⁴³ and Cebpα GMP ChIP-Seq read coverage included at the same locations. Color scale shows Log2 + 1 normalized read counts. d Average peak height (top) and max peak height distribution (bottom) of distal ATAC-Seq peaks relating to (c). e UCSC browser tracks (mm9 murine genome) of Scl:Cdx2 and Scl-Cre ATAC-Seq peaks, and Cdx2-FLAG and Empty vector (EV) ChIP-Seq peaks in HoxA and HoxB clusters. Peaks called by MACS2. Light blue vertical bars highlight Scl:Cdx2 gained peaks positioned with a Cdx2 ChIP-Seq peak and Cdx2 motif. Statistical analyses for (d) performed using two-tailed Mann–Whitney test without adjustment for multiple comparisons. **P < 0.01, ****P < 0.0001.